Genetic variation in the bovine heat shock protein gene in Indonesian Bali cattle (Bos javanicus): A marker candidate for heat stress tolerance trait.

Abstract

Background: Heat stress has a significant impact on cattle performance, particularly in hot-humid climates like tropical regions. Bali cattle (Bos javanicus), an indigenous Indonesian breed, are widely known for their ability to adapt to and withstand heat stress. The heat shock protein (HSP) gene family is responsible for heat stress adaptation, and genetic diversity is linked to the ability of animals to cope with heat stress.

Aims: The purpose of this study was to investigate the genetic variation of potential HSP gene candidates in Bali cattle by scanning single-nucleotide polymorphisms (SNPs) and comparing them to the available cattle genetic reference database.

Methods: The research was divided into two experimental phases. The first step is to identify potential HSP gene candidates in silico. The selected genes were then mapped to the B. javanicus sequence (year 2023 version) to generate primers that were used to amplify all exons for SNP scanning. In the second experiment, a pool of DNA samples was amplified using a custom-designed primer, followed by sequencing and polymorphism analysis. The SNP variation was identified by comparing the nucleotide sequences with the existing Bos taurus and Bos indicus databases at the National Center for Biotechnology Information, which serve as genetic references. Genetic variations were then grouped, classified, and analyzed based on the type of nucleotide mutation and amino acid type.

Results: The results revealed that among the HSP genes in B. javanicus, HSP90AB1 had the highest similarity to those in other breeds: 99.05% similarity with B. taurus and 99.05% with B. indicus. In total, 127 SNPs of the HSP90AB1 gene were identified across exons 2 to 6 of the Bali cattle and have the potential to affect protein function and expression related to cattle traits.

Conclusion: HSP90AB1 can be a candidate gene for thermotolerance trait selection in Bali cattle but needs further study to be used as a selection marker.